Early mammalian embryos undergo remarkable changes in their metabolism, with a global transition from oxidative phosphorylation to glycolysis as they transit out of pluripotency and begin to make the first cell fate decisions in preparation for gastrulation. In humans this transition can be modelled with pluripotent cells in culture which exist in a naive (more pluripotent) and a primed (epiblast like) state and show the same differences in metabolic regulation. These two cell states also show major differences in their epigenetic landscape including in DNA methylation, repressive histone modifications, and spatial organisation of chromatin. I am interested in studying this metabolic regulation and its potential interface with epigenetic modifiers. In order to study metabolic regulation and heterogeneity within populations of naive and primed cells, I have adapted an existing method of constraint-based modelling to using constraints based on single cell RNA-seq data. The implementation of single cell models allows us to directly investigate the effect of transcriptional variability on the metabolism of the cells. Analysis of these modelling results shows that PCA of all reaction fluxes reveals clear differences between naive and primed cells, but interestingly also reveals subgroups within each cell type which exhibit different metabolic landscapes, which has not been previously observed. Notably, we have identified two genes which clearly identify these subgroups: SLC15A1 and SLC15A2. These genes encode transporters which are involved in uptake of dietary peptides, and there is no documentation of their function in pluripotency. Here we use several experimental techniques, including single molecule RNA fluorescence in situ hybridisation, to identify if these subpopulations present as our model suggests; future investigation may lead to novel insights into the regulation of these genes and their previously unnoticed role in stem cell metabolism and pluripotency.